From a88bb1edee1d3e32c3fa808f0ca1cb89c66c6776 Mon Sep 17 00:00:00 2001
From: Henrik Baktoft <hba@aqua.dtu.dk>
Date: Fri, 20 Oct 2023 12:45:02 +0200
Subject: [PATCH] too many adjustments...

---
 DESCRIPTION                |   4 +-
 NAMESPACE                  |   3 +
 R/checkHydros.R            |  21 +++
 R/checkInp.R               |  15 +-
 R/checkInpSync.R           |  30 ----
 R/getBounds.R              |  54 +++++++
 R/getDatTmb.R              |  83 +++++++++++
 R/getDistMat.R             |   2 +-
 R/getInits.R               |  59 ++++++++
 R/getInp.R                 |   3 +
 R/getInpParams.R           |  14 ++
 R/getParams.R              |  59 ++++++++
 R/getParamsXYFromCOA.R     |  18 +++
 R/getToaRbi.R              | 111 ++++++++++++++
 R/prepTmb.R                | 287 -------------------------------------
 R/removeMultipath.R        |  12 ++
 R/runYaps.R                |   2 +-
 R/sync_checkInpSyncData.R  |  16 +--
 R/sync_checkSyncCoverage.R |  30 ++++
 R/sync_getDatTmbSync.R     |   2 +-
 R/sync_getInpSync.R        |   2 +-
 R/sync_plotSyncCheck.R     |   8 +-
 R/sync_plotSyncNetwork.R   |   8 +-
 R/yapsify.R                |  24 ++--
 man/checkHydros.Rd         |  11 ++
 man/getSyncCoverage.Rd     |   2 +-
 man/getToaRbi.Rd           |  11 ++
 man/removeMultipath.Rd     |  11 ++
 man/yapsify.Rd             |  11 ++
 29 files changed, 555 insertions(+), 358 deletions(-)
 create mode 100644 R/checkHydros.R
 create mode 100644 R/getBounds.R
 create mode 100644 R/getDatTmb.R
 create mode 100644 R/getInits.R
 create mode 100644 R/getInpParams.R
 create mode 100644 R/getParams.R
 create mode 100644 R/getParamsXYFromCOA.R
 create mode 100644 R/getToaRbi.R
 create mode 100644 R/removeMultipath.R
 create mode 100644 R/sync_checkSyncCoverage.R
 create mode 100644 man/checkHydros.Rd
 create mode 100644 man/getToaRbi.Rd
 create mode 100644 man/removeMultipath.Rd
 create mode 100644 man/yapsify.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 9d1093a..87681cc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -12,9 +12,9 @@ License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 LinkingTo: Rcpp, TMB, RcppEigen
-Imports: circular, cowplot, data.table, ggplot2, ggrepel, nloptr, plyr, Rcpp, reshape2, splusTimeSeries, stats, TMB, viridis, zoo
+Imports: circular, cowplot, data.table, ggplot2, ggrepel, nloptr, plyr, Rcpp, reshape2, stats, TMB, viridis, zoo
 Suggests: 
     caTools,
 	covr,
diff --git a/NAMESPACE b/NAMESPACE
index 9fb7add..e53d53c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -4,6 +4,7 @@ export(alignBurstSeq)
 export(applyLinCor)
 export(applySync)
 export(applySync_old)
+export(checkHydros)
 export(checkInp)
 export(checkInpSync)
 export(checkInpSyncData)
@@ -29,6 +30,7 @@ export(getSyncCheckDat)
 export(getSyncCoverage)
 export(getSyncModel)
 export(getSyncToa)
+export(getToaRbi)
 export(getToaYaps)
 export(plotBbox)
 export(plotSyncCheck)
@@ -41,6 +43,7 @@ export(plotSyncNetwork)
 export(plotYaps)
 export(prepDetections)
 export(prepSyncParams)
+export(removeMultipath)
 export(runTmb)
 export(runYaps)
 export(simHydros)
diff --git a/R/checkHydros.R b/R/checkHydros.R
new file mode 100644
index 0000000..e2c9600
--- /dev/null
+++ b/R/checkHydros.R
@@ -0,0 +1,21 @@
+#' Internal function to check hydros data.tables
+#' @export
+checkHydros <- function(hydros){
+	if(is.null(attr(hydros, 'yapsified'))){
+		cat("ERROR: The hydros data.table is not yapsified. Run e.g. hydros <- yapsify(hydros) to do so. \n")
+		stopSilent()
+	}
+	
+	if(!is.null(attr(hydros, 'yapsified')) & attr(hydros, 'yapsified') == FALSE){
+		cat("ERROR: The hydros data.table is not yapsified. Run e.g. hydros <- yapsify(hydros) to do so. \n")
+		stopSilent()
+	}
+	
+	if(length(unique(hydros$h_sn)) != nrow(hydros)){
+		cat("ERROR: At least one hydrophone serial number is used more than once in sync_dat$hydros!\n")
+		stopSilent()
+	}
+
+
+	
+}
\ No newline at end of file
diff --git a/R/checkInp.R b/R/checkInp.R
index 4dcfe44..b4b137e 100644
--- a/R/checkInp.R
+++ b/R/checkInp.R
@@ -10,13 +10,17 @@ checkInp <- function(inp){
 	# only relevant for ping_types 'rbi' and 'pbi'?
 	if(inp$datTmb$pingType != 'sbi'){
 		if(inp$datTmb$rbi_min > min(diff(inp$params$top)))	{
-			print(paste0("WARNING: inp$datTmb$rbi_min > min(diff(inp$params$top)) | ",inp$datTmb$rbi_min," > ",min(diff(inp$params$top)),""))
-			inp$datTmb$rbi_min <- min(diff(inp$params$top)) * 0.90
+			cat(paste0("ERROR: inp$datTmb$rbi_min > min(diff(inp$params$top)) | ",inp$datTmb$rbi_min," > ",min(diff(inp$params$top)),"\n"))
+			# inp$datTmb$rbi_min <- min(diff(inp$params$top)) * 0.90
+			# cat("...inp$datTmb$rbi_min adjusted to ", inp$datTmb$rbi_min, "\n")
+			stopSilent()
 		}
 
 		if(inp$datTmb$rbi_max < max(diff(inp$params$top))){
-			print(paste0("WARNING: inp$datTmb$rbi_max < max(diff(inp$params$top)) | ",inp$datTmb$rbi_max," < ",max(diff(inp$params$top)),""))
-			inp$datTmb$rbi_max <- max(diff(inp$params$top)) * 1.10
+			cat(paste0("ERROR: inp$datTmb$rbi_max < max(diff(inp$params$top)) | ",inp$datTmb$rbi_max," < ",max(diff(inp$params$top)),"\n"))
+			# inp$datTmb$rbi_max <- max(diff(inp$params$top)) * 1.10
+			# cat("...inp$datTmb$rbi_max adjusted to ", inp$datTmb$rbi_max, "\n")
+			stopSilent()
 		}
 	}
 	
@@ -40,7 +44,4 @@ checkInp <- function(inp){
 	}
 	
 	print("Pre-flight checkInp() passed!")
-	
-	return(inp)
-
 }
\ No newline at end of file
diff --git a/R/checkInpSync.R b/R/checkInpSync.R
index 55b196c..e824d59 100644
--- a/R/checkInpSync.R
+++ b/R/checkInpSync.R
@@ -56,33 +56,3 @@ checkInpSync <- function(inp_sync, silent_check){
 	
 }
 
-#' Quick overview to check if all hydros have enough data within each offset period.
-#'
-#' @inheritParams checkInpSync
-#' @param plot Logical indicating whether to plot a visual or not.
-#' @export
-#' @return A data.table containing number of pings included in each hydro x offset combination.
-#' @example man/examples/example-yaps_ssu1.R
-getSyncCoverage <- function(inp_sync, plot=FALSE){
-	toa <- inp_sync$dat_tmb_sync$toa
-	nh <- ncol(toa)
-	offset_idx <- inp_sync$dat_tmb_sync$offset_idx
-
-	toa_long <- data.table::data.table(reshape2::melt(toa))
-	colnames(toa_long) <- c('ping', 'h','toa')
-	toa_long[, offset_idx := rep(offset_idx, nh)]
-	sync_coverage <- data.table::data.table(reshape2::melt(with(toa_long[!is.na(toa)], table(h, offset_idx))))
-	colnames(sync_coverage) <- c('h', 'offset_idx' ,'N')
-	
-	if(plot){
-		p <- ggplot2::ggplot(sync_coverage) 
-		p <- p + geom_point(aes(offset_idx, N), col="steelblue") 
-		p <- p + geom_point(data=sync_coverage[N < 50], aes(offset_idx, N), col="blue", size=2)
-		p <- p + geom_point(data=sync_coverage[N < 10], aes(offset_idx, N), col="orange", size=2)
-		p <- p + geom_point(data=sync_coverage[N <= 5], aes(offset_idx, N), col="red", size=2)
-		p <- p + facet_wrap(~h) + ylim(0, max(sync_coverage$N))
-		print(p)
-	}
-	
-	return(sync_coverage)
-}
\ No newline at end of file
diff --git a/R/getBounds.R b/R/getBounds.R
new file mode 100644
index 0000000..f5dd242
--- /dev/null
+++ b/R/getBounds.R
@@ -0,0 +1,54 @@
+#' Get bounds restricting the optimizer
+#* 
+#' Compile a matrix of lower (bounds[,1]) and upper (bounds[,2]) bounds for the parameters to be estimated.
+#' @param datTmb Object obtained using getDatTmb()
+#' @return Matrix of bounds restricting the optimizer when running runYaps().
+#' @noRd
+getBounds <- function(datTmb) {
+	lu_logD_xy 			<- c(-50,  2)
+	lu_logD_z 			<- c(-50,  2)
+
+	lu_logSigma_toa 	<- c(-12, -2)
+	if(datTmb$Edist[2] == 1){ # mixture
+		lu_logScale 	<- c(-30, 10)
+	} else if (datTmb$Edist[3] == 1) { # t
+		lu_logScale 	<- c(-10,2)
+	}
+	lu_log_t_part 		<- c(-100, 100)
+	if(datTmb$pingType == 'rbi'){
+		lu_logSigma_bi 		<- c(-20, 20)
+	} else {
+		lu_logSigma_bi 		<- c(-20, -2)
+	}
+	lu_logD_v 			<- c(-20,  2)
+
+	bounds <- c()
+	bounds <- rbind(bounds, lu_logD_xy)
+
+	if(datTmb$how_3d == 'est'){
+		bounds <- rbind(bounds, lu_logD_z)
+	}
+
+	if(datTmb$ss_data_what == 'est'){
+		bounds <- rbind(bounds, lu_logD_v)
+	}
+
+	if(datTmb$Edist[1] == 1){
+		bounds <- rbind(bounds, lu_logSigma_toa)
+	} else if(datTmb$Edist[2] == 1){
+		bounds <- rbind(bounds, lu_logSigma_toa, lu_logScale, lu_log_t_part)
+	} else if(datTmb$Edist[3] == 1){
+		bounds <- rbind(bounds, lu_logScale)
+	}
+	
+	if(datTmb$pingType == 'sbi'){
+		bounds <- rbind(bounds, lu_logSigma_bi)
+	} else if (datTmb$pingType == 'rbi'){
+		bounds <- rbind(bounds, lu_logSigma_bi)
+	} else if (datTmb$pingType == 'pbi'){
+		bounds <- rbind(bounds, lu_logSigma_bi)
+	}
+	
+	return(bounds)
+}
+
diff --git a/R/getDatTmb.R b/R/getDatTmb.R
new file mode 100644
index 0000000..60f1547
--- /dev/null
+++ b/R/getDatTmb.R
@@ -0,0 +1,83 @@
+#' Internal function - get data for input to TMB
+#'
+#' Compile data for input to TMB.
+#' @param inp_params Selection of parameters used to setup and run YAPS.
+#' @inheritParams getInp
+#'
+#' @return List for use in TMB.
+#' @noRd
+getDatTmb <- function(hydros, toa, E_dist, n_ss, pingType, rbi_min, rbi_max, ss_data_what, ss_data, biTable, inp_params, z_vec, bbox){
+	T0 <- inp_params$T0
+	Hx0 <- inp_params$Hx0
+	Hy0 <- inp_params$Hy0
+	
+	toa <- toa - T0
+	
+	# allowing slight out-of-bounds BIs
+	rbi_min <- rbi_min - rbi_min * 0.05
+	rbi_max <- rbi_max + rbi_max * 0.05
+	
+	# attempting to make sure toa is oriented correct
+	if(!nrow(toa) == nrow(hydros)){
+		toa <- t(toa)
+	}
+
+	if(n_ss > 1){
+		ss_idx <- cut(1:ncol(toa), n_ss, labels=FALSE) - 1 #-1 because zero-indexing in TMB
+	} else {
+		ss_idx <- rep(0, ncol(toa))
+	}
+	approxBI <- mean(diff(colMeans(toa, na.rm=TRUE), na.rm=TRUE), na.rm=TRUE)
+
+	if(ss_data_what == 'data') { stopifnot(length(ss_data) == ncol(toa))}
+
+	Edist <- rep(0,3)
+	if(E_dist == "Gaus") {Edist[1] <- 1}
+	if(E_dist == "Mixture") {Edist[2] <- 1}
+	if(E_dist == "t") {Edist[3] <- 1}
+	
+	if(is.null(z_vec)){
+		how_3d <- 'none'
+		z_vec <- c(1)
+	} else if(z_vec[1] == "est") {
+		how_3d <- 'est'
+		z_vec <- c(1)
+	} else {
+		how_3d <- 'data'
+	}
+	
+	if(is.null(bbox)){
+		bbox <- NA
+	} else {
+		bbox[1] <- bbox[1] - inp_params$Hx0
+		bbox[2] <- bbox[2] - inp_params$Hx0
+		bbox[3] <- bbox[3] - inp_params$Hy0
+		bbox[4] <- bbox[4] - inp_params$Hy0
+	}
+
+	datTmb <- list(
+		model = "yaps_track",
+		H = matrix(c(hydros$h_x-Hx0, hydros$h_y-Hy0, hydros$h_z), ncol=3),
+		nh = nrow(hydros),
+		np = ncol(toa),
+		Edist = Edist,
+		toa = toa,
+		bi_epsilon = 1E-6,
+		bi_penalty = 1E9,
+		rbi_min = rbi_min,
+		rbi_max = rbi_max,
+		pingType = pingType,
+		n_ss = n_ss,
+		ss_idx = ss_idx,
+		ss_data_what = ss_data_what,
+		ss_data = ss_data,
+		approxBI = approxBI,
+		biTable = c(1),
+		how_3d = how_3d,
+		z_vec = z_vec,
+		bbox = bbox
+	)
+	if(pingType == 'pbi') {datTmb$biTable = biTable}
+
+	return(datTmb)
+}
diff --git a/R/getDistMat.R b/R/getDistMat.R
index 600c7be..4f128d0 100644
--- a/R/getDistMat.R
+++ b/R/getDistMat.R
@@ -6,7 +6,7 @@ getDistMat <- function(hydros){
 	colnames(dist_mat) <- hydros$h_sn
 	for(hx in 1:nrow(hydros)){
 		for(hy in 1:nrow(hydros)){
-			dist_mat[hx, hy] <- sqrt((hydros[hx, x] - hydros[hy, x] )^2 + (hydros[hx, y] - hydros[hy, y] )^2 + (hydros[hx, z] - hydros[hy, z] )^2)
+			dist_mat[hx, hy] <- sqrt((hydros[hx, h_x] - hydros[hy, h_x] )^2 + (hydros[hx, h_y] - hydros[hy, h_y] )^2 + (hydros[hx, h_z] - hydros[hy, h_z] )^2)
 		}
 	}
 	return(dist_mat)
diff --git a/R/getInits.R b/R/getInits.R
new file mode 100644
index 0000000..bdb768f
--- /dev/null
+++ b/R/getInits.R
@@ -0,0 +1,59 @@
+#' Get inits for use in TMB
+#'
+#' Compile a vector of initial values to use in TMB. One value for each estimated parameter (not random effects).
+#' Should all be in a credible range.
+#' @param datTmb Object obtained using getDatTmb()
+#' @inheritParams getInp
+#' @return Vector of initial values to use in TMB
+#' @noRd
+getInits <- function(datTmb, sdInits=1) {
+	init_logD_xy <- -1
+
+	if(datTmb$pingType == 'sbi') {
+		init_logSigma_bi <- -6
+	} else if(datTmb$pingType == 'rbi'){
+		if(datTmb$rbi_max >= 10){
+			init_logSigma_bi <- 4 
+		} else {
+			init_logSigma_bi <- -3
+		}
+	} else if(datTmb$pingType == 'pbi'){
+		init_logSigma_bi <- -5
+	}
+	
+	init_logD_v <- 0
+	init_logSigma_toa <- -3 # used in Gaussian and mixture
+	init_logScale <- 1		# used in mixture and pure t
+	init_log_t_part <- -4	# only used in mixture
+
+	inits <- c(init_logD_xy)
+
+	if(datTmb$how_3d == 'est'){
+		init_logD_z <- 0
+		inits <- c(inits, init_logD_z)
+	}
+	
+	if(datTmb$ss_data_what == 'est'){
+		inits <- c(inits, init_logD_v)
+	}
+	
+
+	if(datTmb$Edist[1] == 1){
+		inits <- c(inits, init_logSigma_toa)
+	} else if(datTmb$Edist[2] == 1){
+		inits <- c(inits, init_logSigma_toa, init_logScale, init_log_t_part)
+	} else if(datTmb$Edist[3] == 1){
+		inits <- c(inits, init_logScale)
+	}
+	
+	if(datTmb$pingType == 'sbi'){
+		inits <- c(inits, init_logSigma_bi)#,  init_logD_v)#, init_logSigma_toa, init_logScale, init_log_t_part)
+	} else if (datTmb$pingType == 'rbi'){
+		inits <- c(inits, init_logSigma_bi)#, 					init_logD_v)#, init_logSigma_toa, init_logScale, init_log_t_part)
+	} else if (datTmb$pingType == 'pbi'){
+		inits <- c(inits, init_logSigma_bi)#,  init_logD_v)#, init_logSigma_toa, init_logScale, init_log_t_part)
+	}
+	
+	inits <- stats::rnorm(length(inits), mean=inits, sd=sdInits)
+	return(inits)
+}
diff --git a/R/getInp.R b/R/getInp.R
index ce98ff3..95660d9 100644
--- a/R/getInp.R
+++ b/R/getInp.R
@@ -19,6 +19,9 @@
 #' @example man/examples/example-yaps_ssu1.R
 getInp <- function(hydros, toa, E_dist, n_ss, pingType, sdInits=1, rbi_min=0, rbi_max=0, ss_data_what='est', ss_data=0, biTable=NULL, z_vec=NULL, bbox=NULL){
 	stopifnot(pingType %in% c('sbi', 'pbi', 'rbi'))
+	
+	checkHydros(hydros)
+	
 	inp_params 	<- getInpParams(hydros, toa, pingType)
 	datTmb 		<- getDatTmb(hydros, toa, E_dist, n_ss, pingType, rbi_min, rbi_max, ss_data_what, ss_data, biTable, inp_params, z_vec, bbox)
 	params 		<- getParams(datTmb)
diff --git a/R/getInpParams.R b/R/getInpParams.R
new file mode 100644
index 0000000..78dcf9c
--- /dev/null
+++ b/R/getInpParams.R
@@ -0,0 +1,14 @@
+#' Get parameters for this specific data set
+#'
+#' Compile a list of relevant parameters (e.g. T0) to use later on
+#' @inheritParams getInp
+#' @noRd
+getInpParams <- function(hydros, toa, pingType){
+	T0 <- min(toa, na.rm=TRUE)
+		
+	Hx0 <- hydros[1,h_x]
+	Hy0 <- hydros[1,h_y]
+
+	return(list(T0=T0, Hx0=Hx0, Hy0=Hy0))
+
+}
\ No newline at end of file
diff --git a/R/getParams.R b/R/getParams.R
new file mode 100644
index 0000000..12ae007
--- /dev/null
+++ b/R/getParams.R
@@ -0,0 +1,59 @@
+#' Internal function - get params-list for use in TMB
+#'
+#' Compile a list of parameters for use in TMB.
+#' @param datTmb Object obtained using getDatTmb()
+#' @return List of params for use in TMB
+#' @noRd
+getParams <- function(datTmb){
+	params_XY <- yaps:::getParamsXYFromCOA(datTmb)
+	out <- list(
+		  X = params_XY$X + stats::rnorm(ncol(datTmb$toa), sd=10)
+		, Y = params_XY$Y + stats::rnorm(ncol(datTmb$toa), sd=10)
+		  # X = 0 + stats::rnorm(ncol(datTmb$toa), sd=10)
+		# , Y = 0 + stats::rnorm(ncol(datTmb$toa), sd=10)
+		, top = zoo::na.approx(apply(datTmb$toa, 2, function(k) {stats::median(k, na.rm=TRUE)}), rule=2)	#time of ping
+		# , SS=stats::rnorm(datTmb$n_ss, 1450, 5) 	#speed of sound
+		, logD_xy = 0				#diffusivity of transmitter movement (D_xy in ms)
+		# , logD_v = 0				#diffusivity of speed of sound (D_v in ms)
+		# , logSigma_toa = 0			#sigma for Gaussian
+		# , logScale = 0				#scale parameter for t-distribution
+		# , log_t_part = 0				#Mixture ratio between Gaussian and t
+	)
+	
+	# # # If estimating 3D	
+	if(datTmb$how_3d == "est"){
+		out$Z <- stats::runif(ncol(datTmb$toa), -10, 0)
+		out$logD_z <- 0				#diffusivity of transmitter vertical movement (D_z in ms)
+	}
+	
+
+	# # # ss related
+	if(datTmb$ss_data_what == 'est'){
+		out$logD_v <- 0				#diffusivity of speed of sound (D_v in ms)
+		out$SS <- stats::rnorm(datTmb$n_ss, 1450, 5) 	#speed of sound
+	}
+	
+	# # # Edist related
+	if(datTmb$Edist[1] == 1){
+		out$logSigma_toa = 0			#sigma for Gaussian
+	} else if(datTmb$Edist[2] == 1){
+		out$logSigma_toa = 0			#sigma for Gaussian
+		out$logScale = 0				#scale parameter for t-distribution
+		out$log_t_part = 0				#Mixture ratio between Gaussian and t
+	} else if(datTmb$Edist[3] == 1){
+		out$logScale = 0				#scale parameter for t-distribution
+	}
+
+	# # # Ping type related
+	if(datTmb$pingType %in% c('sbi', 'sbi_double', 'rbi')){
+		out$logSigma_bi <- 0			#sigma  burst interval (sigma_bi in ms)
+	}
+	
+	if(datTmb$pingType == 'pbi'){
+		out$logSigma_bi <- 0			#sigma  burst interval (sigma_bi in ms)
+		out$tag_drift <- stats::rnorm(datTmb$np, 0, 1e-2)
+	}
+
+	
+	return(out)
+}
diff --git a/R/getParamsXYFromCOA.R b/R/getParamsXYFromCOA.R
new file mode 100644
index 0000000..2175756
--- /dev/null
+++ b/R/getParamsXYFromCOA.R
@@ -0,0 +1,18 @@
+#' Internal function - get initial values for X and Y based on Center Of Activity - i.e. hydrophones positions
+#'
+#' Attempts to give meaningful initial values for X and Y based on which hydros detected each ping
+#' @inheritParams getInp
+#' @noRd
+getParamsXYFromCOA <- function(datTmb){
+	toa <- datTmb$toa
+	hydros <- datTmb$H
+
+	toa_detect <- toa
+	toa_detect[!is.na(toa_detect)] <- 1
+
+	X <- zoo::na.approx(colMeans((toa_detect) * hydros[,1], na.rm=TRUE))
+	Y <- zoo::na.approx(colMeans((toa_detect) * hydros[,2], na.rm=TRUE))
+	
+	return(list(X=X, Y=Y))
+
+}
diff --git a/R/getToaRbi.R b/R/getToaRbi.R
new file mode 100644
index 0000000..a1f5af5
--- /dev/null
+++ b/R/getToaRbi.R
@@ -0,0 +1,111 @@
+#' Get TOA matrix for random burst interval transmitters
+#' @export
+getToaRbi <- function(dets, hydros, rbi_min, rbi_max){
+	
+	data.table::setorder(dets, eposync)
+	
+	dets <- merge(dets, hydros[, .(h_sn, h_idx)], all.x=TRUE)
+	
+	# # # TODO
+	# # # Consider to add a better function to remove too short BIs...
+	# # # ...current version is blind to e.g. nobs
+	
+	
+	# remove multipath...
+	dets <- removeMultipath(dets, mp_threshold=0.5)
+	
+	# build seq to catch pings
+	seq_factor <- ifelse(rbi_min < 10, 0.1, 1.0)
+	seq <- matrix(seq(from=floor(min(dets$eposync)), to=ceiling(max(dets$eposync)), by=seq_factor))
+	nobs <- apply(seq, 1, function(k) nrow(dets[eposync %between% c(k-.5*seq_factor, k+.5*seq_factor)]))
+
+	# which times along seq have pings
+	hits <- data.table(epo = seq[nobs > 0], nobs=nobs[nobs > 0])
+	
+	# identify lines representing new pings
+	# threshold for new ping is dependent on rbi_min. For very fast transmitters, we need a lower threshold
+	# threshold could be based on some metric of max possible distance in area...?
+	new_ping_thres <- ifelse(rbi_min >= 5, 1, .5) 
+	if(rbi_min >= 2){
+		hits[, new_ping := c(1, ifelse(diff(epo) > new_ping_thres, 1, 0))]
+	} else {
+		hits[, new_ping := c(1, ifelse(diff(epo) > new_ping_thres, 1, 0))]
+	}
+
+	hits[, ping := cumsum(new_ping)]
+
+	# identify median time for each ping
+	ping_times <- hits[, .(t_ping = median(epo), nobs=sum(nobs)), by=ping]
+
+	# prep to roll hits and dets
+	ping_times[, roll_ping_times := t_ping]
+	dets[, roll_dat := eposync]
+	setkey(dets, roll_dat)
+	setkey(ping_times, roll_ping_times)
+
+	dets[, ping := ping_times[dets, roll="nearest"]	[, ping]	]
+	dets[, roll_dat := NULL]
+	
+	# pings only detected by one hydro are useless for ping_type = rbi
+	# excluded as they might as well be noise
+	dets <- dets[!ping %in% dets[, .N, by=ping][N <= 1, ping]]
+
+	# take the first if more than one detection from one hydro per ping has survived so far...
+	dets <- dets[, .(eposync=min(eposync)), by=.(h_idx, ping)]
+	
+	# ...re-adjust ping number to start from 1 and be continous
+	dets[, new_ping := ping != shift(ping, type="lag")]
+	dets[1, new_ping := TRUE]
+	dets[, ping := cumsum(new_ping)]
+	dets[, new_ping := NULL]
+	
+
+	# identify and remove pings with too short BIs
+	ping_times2 <- dets[, .(ping_time=median(eposync), .N), by=ping]
+	ping_times2[, ping_diff := c(diff(ping_time), NA)]
+	if(rbi_min > 5){
+		ping_times2[, next_ping_too_soon := ping_diff < rbi_min-1]
+	} else {
+		ping_times2[, next_ping_too_soon := ping_diff < rbi_min-.5]
+	}
+	
+	dets <- dets[ping %in% ping_times2[next_ping_too_soon == FALSE, ping]]
+
+	# ...re-adjust ping number to start from 1 and be continous
+	dets[, new_ping := ping != shift(ping, type="lag")]
+	dets[1, new_ping := TRUE]
+	dets[, ping := cumsum(new_ping)]
+	dets[, new_ping := NULL]
+
+	
+	# build toa matrix
+	dets[, h_idx_factor := factor(h_idx, levels=(1:nrow(hydros)))]
+	toa <- as.matrix(reshape2::acast(dets, ping~h_idx_factor, value.var="eposync", drop=FALSE))
+	dets[, h_idx_factor := NULL]
+	
+
+	# remake toa-matrix to include pings missed by all hydros...
+	pings <- dets[, .(top=median(eposync)), by=ping]
+	pings[, diff := c(diff(top), NA)]
+	pings[, ping2next := 1]
+	
+	if(rbi_max > 10){
+		pings[, next_ping_too_late := diff > rbi_max+1] 
+	} else {
+		pings[, next_ping_too_late := diff > rbi_max+.5]
+	}
+	
+	pings[next_ping_too_late==TRUE, ping2next:=ceiling(diff/(rbi_max-1))] 
+
+	pings[, ping_idx:=cumsum(c(1,ping2next[-.N]))]
+
+	toa_all <- matrix(ncol=ncol(toa), nrow=max(pings$ping_idx))
+	toa_all[pings$ping_idx, ] <- toa
+	
+	toa <- toa_all
+	
+	diff(rowMeans(toa, na.rm=TRUE))
+	
+	# print(p1)
+	return(toa)
+}
diff --git a/R/prepTmb.R b/R/prepTmb.R
index 7ebd969..fd40910 100644
--- a/R/prepTmb.R
+++ b/R/prepTmb.R
@@ -1,291 +1,4 @@
-#' Internal function - get data for input to TMB
-#'
-#' Compile data for input to TMB.
-#' @param inp_params Selection of parameters used to setup and run YAPS.
-#' @inheritParams getInp
-#'
-#' @return List for use in TMB.
-#' @noRd
-getDatTmb <- function(hydros, toa, E_dist, n_ss, pingType, rbi_min, rbi_max, ss_data_what, ss_data, biTable, inp_params, z_vec, bbox){
-	T0 <- inp_params$T0
-	Hx0 <- inp_params$Hx0
-	Hy0 <- inp_params$Hy0
-	
-	toa <- toa - T0
-	
-	# allowing slight out-of-bounds BIs
-	rbi_min <- rbi_min - rbi_min * 0.05
-	rbi_max <- rbi_max + rbi_max * 0.05
-	
-	# attempting to make sure toa is oriented correct
-	if(!nrow(toa) == nrow(hydros)){
-		toa <- t(toa)
-	}
 
-	if(n_ss > 1){
-		ss_idx <- cut(1:ncol(toa), n_ss, labels=FALSE) - 1 #-1 because zero-indexing in TMB
-	} else {
-		ss_idx <- rep(0, ncol(toa))
-	}
-	approxBI <- mean(diff(colMeans(toa, na.rm=TRUE), na.rm=TRUE), na.rm=TRUE)
 
-	if(ss_data_what == 'data') { stopifnot(length(ss_data) == ncol(toa))}
 
-	Edist <- rep(0,3)
-	if(E_dist == "Gaus") {Edist[1] <- 1}
-	if(E_dist == "Mixture") {Edist[2] <- 1}
-	if(E_dist == "t") {Edist[3] <- 1}
-	
-	if(is.null(z_vec)){
-		how_3d <- 'none'
-		z_vec <- c(1)
-	} else if(z_vec[1] == "est") {
-		how_3d <- 'est'
-		z_vec <- c(1)
-	} else {
-		how_3d <- 'data'
-	}
-	
-	if(is.null(bbox)){
-		bbox <- NA
-	} else {
-		bbox[1] <- bbox[1] - inp_params$Hx0
-		bbox[2] <- bbox[2] - inp_params$Hx0
-		bbox[3] <- bbox[3] - inp_params$Hy0
-		bbox[4] <- bbox[4] - inp_params$Hy0
-	}
 
-	datTmb <- list(
-		model = "yaps_track",
-		H = matrix(c(hydros$hx-Hx0, hydros$hy-Hy0, hydros$hz), ncol=3),
-		nh = nrow(hydros),
-		np = ncol(toa),
-		Edist = Edist,
-		toa = toa,
-		bi_epsilon = 1E-6,
-		bi_penalty = 1E9,
-		rbi_min = rbi_min,
-		rbi_max = rbi_max,
-		pingType = pingType,
-		n_ss = n_ss,
-		ss_idx = ss_idx,
-		ss_data_what = ss_data_what,
-		ss_data = ss_data,
-		approxBI = approxBI,
-		biTable = c(1),
-		how_3d = how_3d,
-		z_vec = z_vec,
-		bbox = bbox
-	)
-	if(pingType == 'pbi') {datTmb$biTable = biTable}
-
-	return(datTmb)
-}
-
-#' Internal function - get params-list for use in TMB
-#'
-#' Compile a list of parameters for use in TMB.
-#' @param datTmb Object obtained using getDatTmb()
-#' @return List of params for use in TMB
-#' @noRd
-getParams <- function(datTmb){
-	params_XY <- getParamsXYFromCOA(datTmb)
-	out <- list(
-		  X = params_XY$X + stats::rnorm(ncol(datTmb$toa), sd=10)
-		, Y = params_XY$Y + stats::rnorm(ncol(datTmb$toa), sd=10)
-		  # X = 0 + stats::rnorm(ncol(datTmb$toa), sd=10)
-		# , Y = 0 + stats::rnorm(ncol(datTmb$toa), sd=10)
-		, top = zoo::na.approx(apply(datTmb$toa, 2, function(k) {stats::median(k, na.rm=TRUE)}), rule=2)	#time of ping
-		# , SS=stats::rnorm(datTmb$n_ss, 1450, 5) 	#speed of sound
-		, logD_xy = 0				#diffusivity of transmitter movement (D_xy in ms)
-		# , logD_v = 0				#diffusivity of speed of sound (D_v in ms)
-		# , logSigma_toa = 0			#sigma for Gaussian
-		# , logScale = 0				#scale parameter for t-distribution
-		# , log_t_part = 0				#Mixture ratio between Gaussian and t
-	)
-	
-	# # # If estimating 3D	
-	if(datTmb$how_3d == "est"){
-		out$Z <- stats::runif(ncol(datTmb$toa), -10, 0)
-		out$logD_z <- 0				#diffusivity of transmitter vertical movement (D_z in ms)
-	}
-	
-
-	# # # ss related
-	if(datTmb$ss_data_what == 'est'){
-		out$logD_v <- 0				#diffusivity of speed of sound (D_v in ms)
-		out$SS <- stats::rnorm(datTmb$n_ss, 1450, 5) 	#speed of sound
-	}
-	
-	# # # Edist related
-	if(datTmb$Edist[1] == 1){
-		out$logSigma_toa = 0			#sigma for Gaussian
-	} else if(datTmb$Edist[2] == 1){
-		out$logSigma_toa = 0			#sigma for Gaussian
-		out$logScale = 0				#scale parameter for t-distribution
-		out$log_t_part = 0				#Mixture ratio between Gaussian and t
-	} else if(datTmb$Edist[3] == 1){
-		out$logScale = 0				#scale parameter for t-distribution
-	}
-
-	# # # Ping type related
-	if(datTmb$pingType %in% c('sbi', 'sbi_double', 'rbi')){
-		out$logSigma_bi <- 0			#sigma  burst interval (sigma_bi in ms)
-	}
-	
-	if(datTmb$pingType == 'pbi'){
-		out$logSigma_bi <- 0			#sigma  burst interval (sigma_bi in ms)
-		out$tag_drift <- stats::rnorm(datTmb$np, 0, 1e-2)
-	}
-
-	
-	return(out)
-}
-
-#' Internal function - get initial values for X and Y based on Center Of Activity - i.e. hydrophones positions
-#'
-#' Attempts to give meaningful initial values for X and Y based on which hydros detected each ping
-#' @inheritParams getInp
-#' @noRd
-getParamsXYFromCOA <- function(datTmb){
-	toa <- datTmb$toa
-	hydros <- datTmb$H
-
-	toa_detect <- toa
-	toa_detect[!is.na(toa_detect)] <- 1
-
-	X <- zoo::na.approx(colMeans((toa_detect) * hydros[,1], na.rm=TRUE))
-	Y <- zoo::na.approx(colMeans((toa_detect) * hydros[,2], na.rm=TRUE))
-	
-	return(list(X=X, Y=Y))
-
-}
-
-#' Get inits for use in TMB
-#'
-#' Compile a vector of initial values to use in TMB. One value for each estimated parameter (not random effects).
-#' Should all be in a credible range.
-#' @param datTmb Object obtained using getDatTmb()
-#' @inheritParams getInp
-#' @return Vector of initial values to use in TMB
-#' @noRd
-getInits <- function(datTmb, sdInits=1) {
-	init_logD_xy <- -1
-
-	if(datTmb$pingType == 'sbi') {
-		init_logSigma_bi <- -6
-	} else if(datTmb$pingType == 'rbi'){
-		if(datTmb$rbi_max >= 10){
-			init_logSigma_bi <- 4 
-		} else {
-			init_logSigma_bi <- -3
-		}
-	} else if(datTmb$pingType == 'pbi'){
-		init_logSigma_bi <- -5
-	}
-	
-	init_logD_v <- 0
-	init_logSigma_toa <- -3 # used in Gaussian and mixture
-	init_logScale <- 1		# used in mixture and pure t
-	init_log_t_part <- -4	# only used in mixture
-
-	inits <- c(init_logD_xy)
-
-	if(datTmb$how_3d == 'est'){
-		init_logD_z <- 0
-		inits <- c(inits, init_logD_z)
-	}
-	
-	if(datTmb$ss_data_what == 'est'){
-		inits <- c(inits, init_logD_v)
-	}
-	
-
-	if(datTmb$Edist[1] == 1){
-		inits <- c(inits, init_logSigma_toa)
-	} else if(datTmb$Edist[2] == 1){
-		inits <- c(inits, init_logSigma_toa, init_logScale, init_log_t_part)
-	} else if(datTmb$Edist[3] == 1){
-		inits <- c(inits, init_logScale)
-	}
-	
-	if(datTmb$pingType == 'sbi'){
-		inits <- c(inits, init_logSigma_bi)#,  init_logD_v)#, init_logSigma_toa, init_logScale, init_log_t_part)
-	} else if (datTmb$pingType == 'rbi'){
-		inits <- c(inits, init_logSigma_bi)#, 					init_logD_v)#, init_logSigma_toa, init_logScale, init_log_t_part)
-	} else if (datTmb$pingType == 'pbi'){
-		inits <- c(inits, init_logSigma_bi)#,  init_logD_v)#, init_logSigma_toa, init_logScale, init_log_t_part)
-	}
-	
-	inits <- stats::rnorm(length(inits), mean=inits, sd=sdInits)
-	return(inits)
-}
-
-#' Get bounds restricting the optimizer
-#* 
-#' Compile a matrix of lower (bounds[,1]) and upper (bounds[,2]) bounds for the parameters to be estimated.
-#' @param datTmb Object obtained using getDatTmb()
-#' @return Matrix of bounds restricting the optimizer when running runYaps().
-#' @noRd
-getBounds <- function(datTmb) {
-	lu_logD_xy 			<- c(-50,  2)
-	lu_logD_z 			<- c(-50,  2)
-
-	lu_logSigma_toa 	<- c(-12, -2)
-	if(datTmb$Edist[2] == 1){ # mixture
-		lu_logScale 	<- c(-30, 10)
-	} else if (datTmb$Edist[3] == 1) { # t
-		lu_logScale 	<- c(-10,2)
-	}
-	lu_log_t_part 		<- c(-100, 100)
-	if(datTmb$pingType == 'rbi'){
-		lu_logSigma_bi 		<- c(-20, 20)
-	} else {
-		lu_logSigma_bi 		<- c(-20, -2)
-	}
-	lu_logD_v 			<- c(-20,  2)
-
-	bounds <- c()
-	bounds <- rbind(bounds, lu_logD_xy)
-
-	if(datTmb$how_3d == 'est'){
-		bounds <- rbind(bounds, lu_logD_z)
-	}
-
-	if(datTmb$ss_data_what == 'est'){
-		bounds <- rbind(bounds, lu_logD_v)
-	}
-
-	if(datTmb$Edist[1] == 1){
-		bounds <- rbind(bounds, lu_logSigma_toa)
-	} else if(datTmb$Edist[2] == 1){
-		bounds <- rbind(bounds, lu_logSigma_toa, lu_logScale, lu_log_t_part)
-	} else if(datTmb$Edist[3] == 1){
-		bounds <- rbind(bounds, lu_logScale)
-	}
-	
-	if(datTmb$pingType == 'sbi'){
-		bounds <- rbind(bounds, lu_logSigma_bi)
-	} else if (datTmb$pingType == 'rbi'){
-		bounds <- rbind(bounds, lu_logSigma_bi)
-	} else if (datTmb$pingType == 'pbi'){
-		bounds <- rbind(bounds, lu_logSigma_bi)
-	}
-	
-	return(bounds)
-}
-
-#' Get parameters for this specific data set
-#'
-#' Compile a list of relevant parameters (e.g. T0) to use later on
-#' @inheritParams getInp
-#' @noRd
-getInpParams <- function(hydros, toa, pingType){
-	T0 <- min(toa, na.rm=TRUE)
-		
-	Hx0 <- hydros[1,hx]
-	Hy0 <- hydros[1,hy]
-
-	return(list(T0=T0, Hx0=Hx0, Hy0=Hy0))
-
-}
\ No newline at end of file
diff --git a/R/removeMultipath.R b/R/removeMultipath.R
new file mode 100644
index 0000000..49ced33
--- /dev/null
+++ b/R/removeMultipath.R
@@ -0,0 +1,12 @@
+#' Remove multipath detections from detection table
+#' @export
+removeMultipath <- function(dets, mp_threshold=0.5){
+	dets[, epodiff := c(NA, diff(eposync)), by=h_idx]
+	mps <- which(dets$epodiff < mp_threshold)
+	if(length(mps) > 0){
+		dets <- dets[-mps]
+	}
+	dets[, epodiff := NULL]
+	dets[]
+	return(dets)
+}
diff --git a/R/runYaps.R b/R/runYaps.R
index 244ce5d..423d29c 100644
--- a/R/runYaps.R
+++ b/R/runYaps.R
@@ -29,7 +29,7 @@
 runYaps <- function(inp, maxIter=1000, getPlsd=TRUE, getRep=TRUE, silent=TRUE, opt_fun='nlminb', opt_controls=list(), tmb_smartsearch=TRUE){
 	
 	# making sure inp is correct...
-	inp <- checkInp(inp)
+	checkInp(inp)
 	
 	nobs <- z <- z_sd <- NULL
 	print("Running yaps...")
diff --git a/R/sync_checkInpSyncData.R b/R/sync_checkInpSyncData.R
index 4f3a559..52ea297 100644
--- a/R/sync_checkInpSyncData.R
+++ b/R/sync_checkInpSyncData.R
@@ -5,14 +5,12 @@ checkInpSyncData <- function(hydros, dat_sync, dat_ss, sync_params){
 	Es <- 0
 	Ws <- 0
 	
-	if(is.null(attr(hydros, 'yapsified'))){
-		Es <- Es + 1
-		stop("ERROR: The hydros data.table is not yapsified. Run e.g. hydros <- yapsify(hydros) to do so. \n")
-	}
-
-	if(!is.null(attr(hydros, 'yapsified')) & attr(hydros, 'yapsified') == FALSE){
+	checkHydros(hydros)
+	
+	if(nrow(hydros[sync_params$time_keeper %in% h_sn]) == 0){
 		Es <- Es + 1
-		stop("ERROR: The hydros data.table is not yapsified. Run e.g. hydros <- yapsify(hydros) to do so. \n")
+		cat("ERROR: The specified sync_params$time_keeper is not present in hydros. \n")
+		stopSilent()
 	}
 	
 	if(!"epo" %in% colnames(dat_sync)){
@@ -25,10 +23,6 @@ checkInpSyncData <- function(hydros, dat_sync, dat_ss, sync_params){
 		dat_sync[, epofrac := epo+frac]
 	}
 	
-	if(length(unique(hydros$h_sn)) != nrow(hydros)){
-		Es <- Es+1
-		stop("ERROR: At least one hydrophone serial number is used more than once in sync_dat$hydros!\n")
-	}
 	
 	if(sync_params$keep_rate <=0 | (sync_params$keep_rate > 1 & sync_params$keep_rate < 10) | (sync_params$keep_rate >= 10 & sync_params$keep_rate %% 1 != 0)){
 		Es <- Es+1
diff --git a/R/sync_checkSyncCoverage.R b/R/sync_checkSyncCoverage.R
new file mode 100644
index 0000000..59322e3
--- /dev/null
+++ b/R/sync_checkSyncCoverage.R
@@ -0,0 +1,30 @@
+#' Quick overview to check if all hydros have enough data within each offset period.
+#'
+#' @inheritParams checkInpSync
+#' @param plot Logical indicating whether to plot a visual or not.
+#' @export
+#' @return A data.table containing number of pings included in each hydro x offset combination.
+#' @example man/examples/example-yaps_ssu1.R
+getSyncCoverage <- function(inp_sync, plot=FALSE){
+	toa <- inp_sync$dat_tmb_sync$toa
+	nh <- ncol(toa)
+	offset_idx <- inp_sync$dat_tmb_sync$offset_idx
+
+	toa_long <- data.table::data.table(reshape2::melt(toa))
+	colnames(toa_long) <- c('ping', 'h','toa')
+	toa_long[, offset_idx := rep(offset_idx, nh)]
+	sync_coverage <- data.table::data.table(reshape2::melt(with(toa_long[!is.na(toa)], table(h, offset_idx))))
+	colnames(sync_coverage) <- c('h', 'offset_idx' ,'N')
+	
+	if(plot){
+		p <- ggplot2::ggplot(sync_coverage) 
+		p <- p + geom_point(aes(offset_idx, N), col="steelblue") 
+		p <- p + geom_point(data=sync_coverage[N < 50], aes(offset_idx, N), col="blue", size=2)
+		p <- p + geom_point(data=sync_coverage[N < 10], aes(offset_idx, N), col="orange", size=2)
+		p <- p + geom_point(data=sync_coverage[N <= 5], aes(offset_idx, N), col="red", size=2)
+		p <- p + facet_wrap(~h) + ylim(0, max(sync_coverage$N))
+		print(p)
+	}
+	
+	return(sync_coverage)
+}
\ No newline at end of file
diff --git a/R/sync_getDatTmbSync.R b/R/sync_getDatTmbSync.R
index 246f9e6..8617379 100644
--- a/R/sync_getDatTmbSync.R
+++ b/R/sync_getDatTmbSync.R
@@ -4,7 +4,7 @@
 #' @export
 getDatTmbSync <- function(hydros, dat_sync, sync_params, inp_toa_list, offset_vals, T0, ss_vec){
 	# H <- as.matrix(inp_H_info$inp_H)
-	H <- as.matrix(hydros[, .(x,y,z)])
+	H <- as.matrix(hydros[, .(h_x,h_y,h_z)])
 	dimnames(H) <- NULL
 	
 	toa_0 <- inp_toa_list$toa - T0
diff --git a/R/sync_getInpSync.R b/R/sync_getInpSync.R
index 31485c1..469fb9c 100644
--- a/R/sync_getInpSync.R
+++ b/R/sync_getInpSync.R
@@ -95,7 +95,7 @@ getInpSync <- function(hydros, dat_sync, dat_ss=NA, sync_params, plot=TRUE){
 
 	# check to ensure that the timekeeper has data in all offset_idxs
 	dat_tk <- data.table(cbind(toa=inp_toa_list$toa[, colnames(inp_toa_list$toa) == sync_params$time_keeper], offset_idx = factor(dat_tmb_sync$offset_idx)))
-	
+	toa <- inp_toa_list$toa
 	if(nrow(dat_tk[!is.na(toa), .N, by=offset_idx]) != length(unique(dat_tk$offset_idx)) | nrow(dat_tk[!is.na(toa), .N, by=offset_idx][N < 10]) > 0){
 		cat("WARNING: The time keeper should have data (N >= 10) in all offset_idx!\n")
 		cat("...Data in these periods will not be synced!\n")
diff --git a/R/sync_plotSyncCheck.R b/R/sync_plotSyncCheck.R
index 29987b8..f1116f3 100644
--- a/R/sync_plotSyncCheck.R
+++ b/R/sync_plotSyncCheck.R
@@ -56,14 +56,14 @@ plotSyncCheck <- function(sync_model, type=1){
 	if(type == 4){
 		dat_plot4 <- sync_check_dat[, .(mean=mean(abs(delta), na.rm=TRUE), median=median(abs(delta), na.rm=TRUE)), by=.(focal_hsn, sync_tag)]
 
-		dat_plot4 <- merge(dat_plot4, hydros[, .(sync_tag, x_from=x, y_from=y)], by.x="sync_tag", by.y="sync_tag")
-		dat_plot4 <- merge(dat_plot4, hydros[, .(h_sn, x_to=x, y_to=y)], by.x="focal_hsn", by.y="h_sn")
+		dat_plot4 <- merge(dat_plot4, hydros[, .(sync_tag, x_from=h_x, y_from=h_y)], by.x="sync_tag", by.y="sync_tag")
+		dat_plot4 <- merge(dat_plot4, hydros[, .(h_sn, x_to=h_x, y_to=h_y)], by.x="focal_hsn", by.y="h_sn")
 
 		p4 <- ggplot2::ggplot() 
-		p4 <- p4 + geom_point(data=hydros, aes(x=x, y=y)) + coord_fixed(ratio=1) 
+		p4 <- p4 + geom_point(data=hydros, aes(x=h_x, y=h_y)) + coord_fixed(ratio=1) 
 		p4 <- p4 + geom_segment(data=dat_plot4, aes(x=x_from, xend=x_to, y=y_from, yend=y_to, col=mean), lwd=1) 
 		p4 <- p4 + viridis::scale_color_viridis(limits=c(0,max(dat_plot4$mean)), name="Mean dev\n(m)")
-		p4 <- p4 + ggrepel::geom_label_repel(data=hydros, aes(x=x, y=y, label=paste0(h_sn,'\n',sync_tag)))
+		p4 <- p4 + ggrepel::geom_label_repel(data=hydros, aes(x=h_x, y=h_y, label=paste0(h_sn,'\n',sync_tag)))
 		return(p4)
 	}
 	
diff --git a/R/sync_plotSyncNetwork.R b/R/sync_plotSyncNetwork.R
index 5a99aa0..bd70217 100644
--- a/R/sync_plotSyncNetwork.R
+++ b/R/sync_plotSyncNetwork.R
@@ -7,12 +7,12 @@ plotSyncNetwork <- function(hydros, dat_sync){
 	}
 	
 	sync_at_hydros <- dat_sync[, .N, by=.(h_sn, tag)]
-	sync_at_hydros <- merge(sync_at_hydros, hydros[, .(sync_tag, x_from=x, y_from=y)], by.x="tag", by.y="sync_tag")
-	sync_at_hydros <- merge(sync_at_hydros, hydros[, .(h_sn, x_to=x, y_to=y)], by="h_sn")
+	sync_at_hydros <- merge(sync_at_hydros, hydros[, .(sync_tag, x_from=h_x, y_from=h_y)], by.x="tag", by.y="sync_tag")
+	sync_at_hydros <- merge(sync_at_hydros, hydros[, .(h_sn, x_to=h_x, y_to=h_y)], by="h_sn")
 
 	p1 <- ggplot2::ggplot() 
-	p1 <- p1 + geom_point(data=hydros, aes(x=x, y=y)) + coord_fixed(ratio=1) 
+	p1 <- p1 + geom_point(data=hydros, aes(x=h_x, y=h_y)) + coord_fixed(ratio=1) 
 	p1 <- p1 + geom_segment(data=sync_at_hydros, aes(x=x_from, xend=x_to, y=y_from, yend=y_to, col=N), lwd=2) + viridis::scale_color_viridis(limits=c(0,max(sync_at_hydros$N)))
-	p1 <- p1 + ggrepel::geom_label_repel(data=hydros, aes(x=x, y=y, label=paste0(h_sn,'\n',sync_tag)))
+	p1 <- p1 + ggrepel::geom_label_repel(data=hydros, aes(x=h_x, y=h_y, label=paste0(h_sn,'\n',sync_tag)))
 	p1
 }
\ No newline at end of file
diff --git a/R/yapsify.R b/R/yapsify.R
index f68d500..03786ad 100644
--- a/R/yapsify.R
+++ b/R/yapsify.R
@@ -1,5 +1,4 @@
 #' Internal function. yapsify / standarize hydros and detections for sync and yaps
-#' @noRd
 #' @export
 yapsify <- function(yapsify_me){
 	
@@ -10,24 +9,33 @@ yapsify <- function(yapsify_me){
 		}
 	}
 	
-	if(sum(c("x", "y", "z") %in% colnames(yapsify_me)) >= 1){ # seems to be a hydro data.table
+	if(sum(c('h_sn', 'h_x','h_y','h_z','sync_tag') %in% colnames(yapsify_me)) != 5 & sum(c('ts','h_sn','tag','frac') %in% colnames(yapsify_me)) != 4){
+		cat("ERROR: Data must contain the following one of the following combinations of colnames:
+			...hydros: c('h_sn', 'h_x', 'h_y', 'h_z', 'sync_tag') 
+			...detections: c('ts', 'h_sn', 'tag', 'frac')
+			...You have colnames(yapsify_me) = ",paste0(colnames(yapsify_me), collapse=", ")	,"
+			")
+		stopSilent()
+	}
+	
+	if(sum(c("h_x", "h_y", "h_z") %in% colnames(yapsify_me)) >= 1){ # seems to be a hydro data.table
 
-		std_h <- yapsify_me[, c('h_sn', 'x','y','z','sync_tag')]
+		std_h <- yapsify_me[, c('h_sn', 'h_x','h_y','h_z','sync_tag')]
 		setorder(std_h, h_sn)
 		std_h[, h_idx := 1:.N]
 
-		Hx0 <- std_h[1,x]
-		Hy0 <- std_h[1,y]
+		Hx0 <- std_h[1,h_x]
+		Hy0 <- std_h[1,h_y]
 		
-		std_h[, x:=x-Hx0]
-		std_h[, y:=y-Hy0]
+		std_h[, h_x:=h_x-Hx0]
+		std_h[, h_y:=h_y-Hy0]
 		std_h[]
 		
 		attr(std_h, 'yapsified') <- TRUE
 		attr(std_h, 'Hx0') <- Hx0
 		attr(std_h, 'Hy0') <- Hy0
 	
-		return(std_h=std_h)
+		return(std_h)
 	} else if(sum(c("ts", "tag", "epo", "frac") %in% colnames(yapsify_me)) >= 1){ # should be a detection table
 		std_dat <- yapsify_me[, c('ts','h_sn','tag','frac')]
 		std_dat[, epo := floor(as.numeric(ts))]
diff --git a/man/checkHydros.Rd b/man/checkHydros.Rd
new file mode 100644
index 0000000..ac64b69
--- /dev/null
+++ b/man/checkHydros.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/checkHydros.R
+\name{checkHydros}
+\alias{checkHydros}
+\title{Internal function to check hydros data.tables}
+\usage{
+checkHydros(hydros)
+}
+\description{
+Internal function to check hydros data.tables
+}
diff --git a/man/getSyncCoverage.Rd b/man/getSyncCoverage.Rd
index 0b41006..ad8912b 100644
--- a/man/getSyncCoverage.Rd
+++ b/man/getSyncCoverage.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/checkInpSync.R
+% Please edit documentation in R/sync_checkSyncCoverage.R
 \name{getSyncCoverage}
 \alias{getSyncCoverage}
 \title{Quick overview to check if all hydros have enough data within each offset period.}
diff --git a/man/getToaRbi.Rd b/man/getToaRbi.Rd
new file mode 100644
index 0000000..2d55953
--- /dev/null
+++ b/man/getToaRbi.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/getToaRbi.R
+\name{getToaRbi}
+\alias{getToaRbi}
+\title{Get TOA matrix for random burst interval transmitters}
+\usage{
+getToaRbi(dets, hydros, rbi_min, rbi_max)
+}
+\description{
+Get TOA matrix for random burst interval transmitters
+}
diff --git a/man/removeMultipath.Rd b/man/removeMultipath.Rd
new file mode 100644
index 0000000..daaf20b
--- /dev/null
+++ b/man/removeMultipath.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/removeMultipath.R
+\name{removeMultipath}
+\alias{removeMultipath}
+\title{Remove multipath detections from detection table}
+\usage{
+removeMultipath(dets, mp_threshold = 0.5)
+}
+\description{
+Remove multipath detections from detection table
+}
diff --git a/man/yapsify.Rd b/man/yapsify.Rd
new file mode 100644
index 0000000..c6121c2
--- /dev/null
+++ b/man/yapsify.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/yapsify.R
+\name{yapsify}
+\alias{yapsify}
+\title{Internal function. yapsify / standarize hydros and detections for sync and yaps}
+\usage{
+yapsify(yapsify_me)
+}
+\description{
+Internal function. yapsify / standarize hydros and detections for sync and yaps
+}